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Bug 822615 - app-doc/doxygen-1.9.2: In file included from /var/tmp/portage/app-doc/doxygen-1.9.2/work/doxygen-1.9.2/src/constexp.l:29: /var/tmp/portage/app-doc/doxygen-1.9.2/work/doxygen-1.9.2/src/constexp.h:19:10: fatal error: 'string' file not found
Summary: app-doc/doxygen-1.9.2: In file included from /var/tmp/portage/app-doc/doxygen...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Matthias Maier
URL:
Whiteboard:
Keywords:
Depends on:
Blocks: systemwide-clang
  Show dependency tree
 
Reported: 2021-11-09 09:57 UTC by Anton Gubarkov
Modified: 2022-05-14 20:40 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---

Attachments
build log (build.log,112.21 KB, text/x-log)
2021-11-09 09:58 UTC, Anton Gubarkov 		Details
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Description Anton Gubarkov 2021-11-09 09:57:16 UTC 
[ 50%] Building CXX object src/CMakeFiles/doxymain.dir/__/generated_src/constexp.cpp.o
cd /var/tmp/portage/app-doc/doxygen-1.9.2/work/doxygen-1.9.2_build/src && /usr/lib/llvm/13/bin/clang++ -DYY_BUF_SIZE=262144 -DYY_READ_BUF_SIZE=262144 -I/var/tmp/portage/app-doc/doxygen-1.9.2/work/doxygen-1.9.2/filesystem -I/var/tmp/portage/app-doc/doxygen-1.9.2/work/doxygen-1.9.2/libmd5 -I/var/tmp/portage/app-doc/doxygen-1.9.2/work/doxygen-1.9.2/liblodepng -I/var/tmp/portage/app-doc/doxygen-1.9.2/work/doxygen-1.9.2/libmscgen -I/var/tmp/portage/app-doc/doxygen-1.9.2/work/doxygen-1.9.2/libversion -I/var/tmp/portage/app-doc/doxygen-1.9.2/work/doxygen-1.9.2/libxml -I/var/tmp/portage/app-doc/doxygen-1.9.2/work/doxygen-1.9.2/vhdlparser -I/var/tmp/portage/app-doc/doxygen-1.9.2/work/doxygen-1.9.2/src -I/var/tmp/portage/app-doc/doxygen-1.9.2/work/doxygen-1.9.2_build/generated_src -I/usr/lib/llvm/13/include  -march=native -O2 -falign-functions=32 -pipe -fvisibility=hidden -fvisibility-inlines-hidden   -D_GNU_SOURCE -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -stdlib=libc++ -Wall -Wextra -Wshadow -Wnon-virtual-dtor -Wcast-align -Wunused -Woverloaded-virtual -Wpedantic -Wconversion -Wnull-dereference -Wdouble-promotion -Wformat=2 -Wno-unused-parameter -Wno-implicit-int-conversion -Wno-sign-conversion -Wno-format-nonliteral -Wno-shorten-64-to-32 -std=gnu++14 -MD -MT src/CMakeFiles/doxymain.dir/__/generated_src/constexp.cpp.o -MF CMakeFiles/doxymain.dir/__/generated_src/constexp.cpp.o.d -o CMakeFiles/doxymain.dir/__/generated_src/constexp.cpp.o -c /var/tmp/portage/app-doc/doxygen-1.9.2/work/doxygen-1.9.2_build/generated_src/constexp.cpp
In file included from /var/tmp/portage/app-doc/doxygen-1.9.2/work/doxygen-1.9.2/src/constexp.l:29:
/var/tmp/portage/app-doc/doxygen-1.9.2/work/doxygen-1.9.2/src/constexp.h:19:10: fatal error: 'string' file not found
#include <string>
         ^~~~~~~~
Comment 1 Anton Gubarkov 2021-11-09 09:57:41 UTC 
PF16W6Y2 ~ # emerge --info
Portage 3.0.28 (python 3.9.8-final-0, default/linux/amd64/17.1/desktop/gnome/systemd, gcc-11.2.0, glibc-2.33-r7, 5.15.1-gentoo x86_64)
=================================================================
System uname: Linux-5.15.1-gentoo-x86_64-Intel-R-_Core-TM-_i7-8850H_CPU_@_2.60GHz-with-glibc2.33
KiB Mem:    32564828 total,    934304 free
KiB Swap:   33554428 total,  30559204 free
Timestamp of repository gentoo: Mon, 08 Nov 2021 22:51:40 +0000
Head commit of repository gentoo: b7d9ade0b35c10d18807c6cf7537b7d2a3beadf4

Head commit of repository audio-overlay: 6a99adb585566300b6c6a47c8253add4ee31b9f2

Head commit of repository lto-overlay: 435a9d968854fef21015796a5f464243dc4caa03

Head commit of repository mv: f889c332974e8a5a9705104d710ff10d7bf0bb6f

sh bash 5.1_p8
ld GNU ld (Gentoo 2.36.1 p4) 2.36.1
ccache version 4.4.2 [disabled]
app-shells/bash:          5.1_p8::gentoo
dev-java/java-config:     2.3.1::gentoo
dev-lang/perl:            5.34.0-r5::gentoo
dev-lang/python:          2.7.18_p13::gentoo, 3.8.12_p1::gentoo, 3.9.8::gentoo, 3.10.0_p1::gentoo
dev-lang/rust:            1.56.1::gentoo
dev-util/ccache:          4.4.2::gentoo
dev-util/cmake:           3.21.4::gentoo
sys-apps/baselayout:      2.8::gentoo
sys-apps/sandbox:         2.29::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.71-r1::gentoo
sys-devel/automake:       1.16.5::gentoo
sys-devel/binutils:       2.36.1-r2::gentoo, 2.37_p1::gentoo
sys-devel/gcc:            8.4.0-r2::gentoo, 10.3.0-r2::gentoo, 11.2.0::gentoo
sys-devel/gcc-config:     2.4::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.3::gentoo
sys-kernel/linux-headers: 5.14::gentoo (virtual/os-headers)
sys-libs/glibc:           2.33-r7::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: git
    sync-uri: git://github.com/gentoo-mirror/gentoo.git
    priority: -1000

audio-overlay
    location: /var/lib/layman/audio-overlay
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/audio-overlay.git
    masters: gentoo
    priority: 50

calculate
    location: /var/lib/layman/calculate
    masters: gentoo
    priority: 50

dlang
    location: /var/lib/layman/dlang
    masters: gentoo
    priority: 50

gentoo-zh
    location: /var/lib/layman/gentoo-zh
    masters: gentoo
    priority: 50

go-overlay
    location: /var/lib/layman/go-overlay
    masters: gentoo
    priority: 50

lto-overlay
    location: /var/lib/layman/lto-overlay
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/lto-overlay.git
    masters: gentoo mv
    priority: 50

mv
    location: /var/lib/layman/mv
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/mv.git
    masters: gentoo
    priority: 50

steam-overlay
    location: /var/lib/layman/steam-overlay
    masters: gentoo
    priority: 50

tlp
    location: /var/lib/layman/tlp
    masters: gentoo
    priority: 50

rugubara
    location: /var/lib/layman/rugubara
    masters: gentoo
    priority: 100

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA Vivaldi"
CBUILD="x86_64-pc-linux-gnu"
CC="clang"
CFLAGS="-march=native -O3 -fno-semantic-interposition -fgraphite-identity -floop-nest-optimize  -flto=12 -fuse-linker-plugin -falign-functions=32 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXX="clang++"
CXXFLAGS="-march=native -O3 -fno-semantic-interposition -fgraphite-identity -floop-nest-optimize  -flto=12 -fuse-linker-plugin -falign-functions=32 -pipe"
DISTDIR="/usr/portage/distfiles"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-march=native -O3 -fno-semantic-interposition -fgraphite-identity -floop-nest-optimize  -flto=12 -fuse-linker-plugin -falign-functions=32 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-march=native -O3 -fno-semantic-interposition -fgraphite-identity -floop-nest-optimize  -flto=12 -fuse-linker-plugin -falign-functions=32 -pipe"
GENTOO_MIRRORS="http://gentoo.bloodhost.ru/ rsync://gentoo.bloodhost.ru/gentoo-distfiles http://ftp.ntua.gr/pub/linux/gentoo/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j6"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac acl acpi aio alsa amd64 ap bash-completion bluetooth branding bzip2 cacert cairo caps cdda cdr cgroup-hybrid chromecast clang cli client colord crypt cups dbus djvu dri dri3 dts dvd dvdr eds egl emboss encode evo exif fat ffmpeg fftw flac fortran gdbm gif gimp gles2 gnome gnome-keyring gnome-online-accounts gpm graphite gstreamer gtk gtk3 gui heif iconv icu introspection io-uring ipv6 jack jpeg jpeg2k lcms libglvnd libnotify libsecret libtirpc libzfs lm_sensors lto lv2 mad mng mp3 mp4 mpeg multilib native-headset nautilus ncat ncurses networkmanager nfs nls nptl ntfs nvenc nvme ogg opencl opengl openmp opus p2p pam pango pcre pdf png policykit ppds pulseaudio qt5 raw readline sdl sdl2 seccomp smp sna sound spell spice split-usr ssl startup-notification svg synaptics sysprof systemd thunderbolt tiff tracker truetype udev udisks uefi unicode upower usb usbredir user-session vaapi vala vdpau virgl vlc vorbis vulkan wayland webdav wireguard wxwidgets x264 x265 xattr xcb xml xv xvid zeroconf zfs zlib" ABI_X86="64" ADA_TARGET="gnat_2019" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput wacom" KERNEL="linux" L10N="en ru" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-3 php7-4" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_9" PYTHON_TARGETS="python3_8 python3_9" RUBY_TARGETS="ruby26 ruby27 ruby27 ruby30" USERLAND="GNU" VIDEO_CARDS="intel i965 iris nvidia" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq proto steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RUSTFLAGS
Comment 2 Anton Gubarkov 2021-11-09 09:58:27 UTC 
Created attachment 749814 [details]
build log
Comment 3 Tee KOBAYASHI 2021-11-10 02:17:14 UTC 
A workaround would be to merge sys-libs/libcxx.

$ egrep -A 1 -B 1 'libc\+\+' doxygen-1.9.2/CMakeLists.txt
if (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
    option(use_libc++  "Use libc++ as C++ standard library." ON)
endif()

IMO we should be able to control "use_libc++" CMake variable from ebuilds.
Comment 4 Sam James archtester Gentoo Infrastructure gentoo-dev Security 2021-11-10 02:26:01 UTC 
(In reply to Tee KOBAYASHI from comment #3)
> A workaround would be to merge sys-libs/libcxx.
> 
> $ egrep -A 1 -B 1 'libc\+\+' doxygen-1.9.2/CMakeLists.txt
> if (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
>     option(use_libc++  "Use libc++ as C++ standard library." ON)
> endif()
> 
> IMO we should be able to control "use_libc++" CMake variable from ebuilds.

Honestly I’d much prefer the build system did nothing here and let the user choose. I’ll rip it out if possible.
Comment 5 Matthias Maier gentoo-dev 2022-05-14 20:19:05 UTC 
I am able to compile doxygen-1.9.3 with USE=clang in a clang/libc++ chroot with the following env/package.env settings:

  CC="clang-13"
  CXX="clang++-13"
  CPP="clang-13 -E"
  CFLAGS="${CFLAGS} -fpic"
  CXXFLAGS="${CXXFLAGS} -fpic -stdlib=libc++ -std=c++14"

# ldd /usr/bin/doxygen 
        linux-vdso.so.1 (0x00007ffc5b9b9000)
        libclang.so.13 => /usr/lib/llvm/14/lib64/libclang.so.13 (0x00007f65b3601000)
        libclang-cpp.so.14libcxx => /usr/lib/llvm/14/lib64/libclang-cpp.so.14libcxx (0x00007f65afe5e000)
        libLLVM-14libcxx.so => /usr/lib/llvm/14/lib64/libLLVM-14libcxx.so (0x00007f65a9a85000)
        libc++.so.1 => /usr/lib64/libc++.so.1 (0x00007f65a9984000)
        libc++abi.so.1 => /usr/lib64/libc++abi.so.1 (0x00007f65a9949000)
        libunwind.so.1 => /usr/lib64/libunwind.so.1 (0x00007f65a993d000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f65a9860000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f65a9669000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f65b5382000)
        libffi.so.8 => /usr/lib64/libffi.so.8 (0x00007f65a965d000)
        libz.so.1 => /lib64/libz.so.1 (0x00007f65a9643000)
        libtinfo.so.6 => /lib64/libtinfo.so.6 (0x00007f65a9604000)
        libgcc_s.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/11.3.0/libgcc_s.so.1 (0x00007f65a95e8000)


Anton, I have the suspicion that there might have been an issue in your toolchain with some accidentally mixed libc++/libstdc++ setup.


(In reply to Sam James from comment #4)
> 
> Honestly I’d much prefer the build system did nothing here and let the user
> choose. I’ll rip it out if possible.

Yes, the build system configuration switch is ugly, but always disabled, so does nothing. It just sets the -std=libc++ flag which can already be achieved by using a proper env/package.env setup.


I will close as "worksforme" for the time being - if there is something that I missed, please reopen!
Comment 6 Matthias Maier gentoo-dev 2022-05-14 20:32:45 UTC 
Ah, it is ON per default. How silly.
Comment 7 Larry the Git Cow gentoo-dev 2022-05-14 20:40:24 UTC 
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=03f0bf4cdacfe0c0ce7fb7e5efe62d2b61b42115

commit 03f0bf4cdacfe0c0ce7fb7e5efe62d2b61b42115
Author:     Matthias Maier <tamiko@gentoo.org>
AuthorDate: 2022-05-14 20:37:58 +0000
Commit:     Matthias Maier <tamiko@gentoo.org>
CommitDate: 2022-05-14 20:40:20 +0000

    app-doc/doxygen: do not force -std=libc++ when compiling with clang
    
    Closes: https://bugs.gentoo.org/822615
    Signed-off-by: Matthias Maier <tamiko@gentoo.org>

 app-doc/doxygen/doxygen-1.9.1.ebuild                        |  1 +
 app-doc/doxygen/doxygen-1.9.2.ebuild                        |  1 +
 app-doc/doxygen/doxygen-1.9.3.ebuild                        |  1 +
 app-doc/doxygen/doxygen-1.9.4.ebuild                        |  1 +
 .../doxygen/files/doxygen-1.9.1-do_not_force_libcxx.patch   | 13 +++++++++++++
 5 files changed, 17 insertions(+)